diff --git a/.gitignore b/.gitignore
index bdfa3322a55a..5131e198399a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,3 +91,4 @@ lib/
 metastore_db
 
 plugin/updater_gpu/test/cpp/data
+/include/xgboost/build_config.h
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7b0d90797a44..061431de5684 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -49,6 +49,26 @@ if(WIN32 AND MINGW)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")
 endif()
 
+# Check existence of software pre-fetching
+include(CheckCXXSourceCompiles)
+check_cxx_source_compiles("
+#include <xmmintrin.h>
+int main() {
+  char data = 0;
+  const char* address = &data;
+  _mm_prefetch(address, _MM_HINT_NTA);
+  return 0;
+}
+" XGBOOST_MM_PREFETCH_PRESENT)
+check_cxx_source_compiles("
+int main() {
+  char data = 0;
+  const char* address = &data;
+  __builtin_prefetch(address, 0, 0);
+  return 0;
+}
+" XGBOOST_BUILTIN_PREFETCH_PRESENT)
+
 # Sanitizer
 if(USE_SANITIZER)
   include(cmake/Sanitizer.cmake)
@@ -82,6 +102,12 @@ include_directories (
     ${PROJECT_SOURCE_DIR}/rabit/include
 )
 
+# Generate configurable header
+set(CMAKE_LOCAL "${PROJECT_SOURCE_DIR}/cmake")
+set(INCLUDE_ROOT "${PROJECT_SOURCE_DIR}/include")
+message(STATUS "${CMAKE_LOCAL}/build_config.h.in -> ${INCLUDE_ROOT}/xgboost/build_config.h")
+configure_file("${CMAKE_LOCAL}/build_config.h.in" "${INCLUDE_ROOT}/xgboost/build_config.h")
+
 file(GLOB_RECURSE SOURCES
     src/*.cc
     src/*.h
diff --git a/cmake/build_config.h.in b/cmake/build_config.h.in
new file mode 100644
index 000000000000..b49dde12e123
--- /dev/null
+++ b/cmake/build_config.h.in
@@ -0,0 +1,7 @@
+#ifndef XGBOOST_BUILD_CONFIG_H_
+#define XGBOOST_BUILD_CONFIG_H_
+
+#cmakedefine XGBOOST_MM_PREFETCH_PRESENT
+#cmakedefine XGBOOST_BUILTIN_PREFETCH_PRESENT
+
+#endif  // XGBOOST_BUILD_CONFIG_H_
diff --git a/include/xgboost/base.h b/include/xgboost/base.h
index 97b140294f22..55c2e4ac7144 100644
--- a/include/xgboost/base.h
+++ b/include/xgboost/base.h
@@ -218,4 +218,8 @@ using bst_omp_uint = dmlc::omp_uint;  // NOLINT
 #endif
 #endif
 }  // namespace xgboost
+
+/* Always keep this #include at the bottom of xgboost/base.h */
+#include <xgboost/build_config.h>
+
 #endif  // XGBOOST_BASE_H_
diff --git a/include/xgboost/build_config.h b/include/xgboost/build_config.h
new file mode 100644
index 000000000000..1e36dc80889c
--- /dev/null
+++ b/include/xgboost/build_config.h
@@ -0,0 +1,20 @@
+/*!
+ * Copyright (c) 2018 by Contributors
+ * \file build_config.h
+ * \brief Fall-back logic for platform-specific feature detection.
+ * \author Hyunsu Philip Cho
+ */
+#ifndef XGBOOST_BUILD_CONFIG_H_
+#define XGBOOST_BUILD_CONFIG_H_
+
+/* default logic for software pre-fetching */
+#if (defined(_MSC_VER) && (defined(_M_IX86) || defined(_M_AMD64))) || defined(__INTEL_COMPILER)
+  // Enable _mm_prefetch for Intel compiler and MSVC+x86
+  #define XGBOOST_MM_PREFETCH_PRESENT
+  #define XGBOOST_BUILTIN_PREFETCH_PRESENT
+#elif defined(__GNUC__)
+  // Enable __builtin_prefetch for GCC
+  #define XGBOOST_BUILTIN_PREFETCH_PRESENT
+#endif
+
+#endif  // XGBOOST_BUILD_CONFIG_H_
diff --git a/src/common/hist_util.cc b/src/common/hist_util.cc
index da6e4d770bff..a988d3baf9ff 100644
--- a/src/common/hist_util.cc
+++ b/src/common/hist_util.cc
@@ -14,6 +14,15 @@
 #include "./hist_util.h"
 #include "./quantile.h"
 
+#if defined(XGBOOST_MM_PREFETCH_PRESENT)
+  #include <xmmintrin.h>
+  #define PREFETCH_READ_T0(addr) _mm_prefetch(reinterpret_cast<const char*>(addr), _MM_HINT_T0)
+#elif defined(XGBOOST_BUILTIN_PREFETCH_PRESENT)
+  #define PREFETCH_READ_T0(addr) __builtin_prefetch(reinterpret_cast<const char*>(addr), 0, 3)
+#else  // no SW pre-fetching available; PREFETCH_READ_T0 is no-op
+  #define PREFETCH_READ_T0(addr) do {} while (0)
+#endif
+
 namespace xgboost {
 namespace common {
 
@@ -399,56 +408,89 @@ void GHistBuilder::BuildHist(const std::vector<GradientPair>& gpair,
                              const RowSetCollection::Elem row_indices,
                              const GHistIndexMatrix& gmat,
                              GHistRow hist) {
-  data_.resize(nbins_ * nthread_, GHistEntry());
-  std::fill(data_.begin(), data_.end(), GHistEntry());
+  const size_t nthread = static_cast<size_t>(this->nthread_);
+  data_.resize(nbins_ * nthread_);
+
+  const size_t* rid =  row_indices.begin;
+  const size_t nrows = row_indices.Size();
+  const uint32_t* index = gmat.index.data();
+  const size_t* row_ptr =  gmat.row_ptr.data();
+  const float* pgh = reinterpret_cast<const float*>(gpair.data());
+
+  double* hist_data = reinterpret_cast<double*>(hist.begin);
+  double* data = reinterpret_cast<double*>(data_.data());
+
+  const size_t block_size = 512;
+  size_t n_blocks = nrows/block_size;
+  n_blocks += !!(nrows - n_blocks*block_size);
+
+  const size_t nthread_to_process = std::min(nthread,  n_blocks);
+  memset(thread_init_.data(), '\0', nthread_to_process*sizeof(size_t));
+
+  const size_t cache_line_size = 64;
+  const size_t prefetch_offset = 10;
+  size_t no_prefetch_size = prefetch_offset + cache_line_size/sizeof(*rid);
+  no_prefetch_size = no_prefetch_size > nrows ? nrows : no_prefetch_size;
+
+  #pragma omp parallel for num_threads(nthread_to_process) schedule(guided)
+  for (bst_omp_uint iblock = 0; iblock < n_blocks; iblock++) {
+    dmlc::omp_uint tid = omp_get_thread_num();
+    double* data_local_hist = ((nthread_to_process == 1) ? hist_data :
+            reinterpret_cast<double*>(data_.data() + tid * nbins_));
+
+    if (!thread_init_[tid]) {
+      memset(data_local_hist, '\0', 2*nbins_*sizeof(double));
+      thread_init_[tid] = true;
+    }
 
-  constexpr int kUnroll = 8;  // loop unrolling factor
-  const auto nthread = static_cast<bst_omp_uint>(this->nthread_);
-  const size_t nrows = row_indices.end - row_indices.begin;
-  const size_t rest = nrows % kUnroll;
+    const size_t istart = iblock*block_size;
+    const size_t iend = (((iblock+1)*block_size > nrows) ? nrows : istart + block_size);
+    for (size_t i = istart; i < iend; ++i) {
+      const size_t icol_start = row_ptr[rid[i]];
+      const size_t icol_end = row_ptr[rid[i]+1];
 
-  #pragma omp parallel for num_threads(nthread) schedule(guided)
-  for (bst_omp_uint i = 0; i < nrows - rest; i += kUnroll) {
-    const bst_omp_uint tid = omp_get_thread_num();
-    const size_t off = tid * nbins_;
-    size_t rid[kUnroll];
-    size_t ibegin[kUnroll];
-    size_t iend[kUnroll];
-    GradientPair stat[kUnroll];
-    for (int k = 0; k < kUnroll; ++k) {
-      rid[k] = row_indices.begin[i + k];
-    }
-    for (int k = 0; k < kUnroll; ++k) {
-      ibegin[k] = gmat.row_ptr[rid[k]];
-      iend[k] = gmat.row_ptr[rid[k] + 1];
-    }
-    for (int k = 0; k < kUnroll; ++k) {
-      stat[k] = gpair[rid[k]];
-    }
-    for (int k = 0; k < kUnroll; ++k) {
-      for (size_t j = ibegin[k]; j < iend[k]; ++j) {
-        const uint32_t bin = gmat.index[j];
-        data_[off + bin].Add(stat[k]);
+      if (i < nrows - no_prefetch_size) {
+        PREFETCH_READ_T0(row_ptr + rid[i + prefetch_offset]);
+        PREFETCH_READ_T0(pgh + 2*rid[i + prefetch_offset]);
+      }
+
+      for (size_t j = icol_start; j < icol_end; ++j) {
+        const uint32_t idx_bin = 2*index[j];
+        const size_t idx_gh = 2*rid[i];
+
+        data_local_hist[idx_bin] += pgh[idx_gh];
+        data_local_hist[idx_bin+1] += pgh[idx_gh+1];
       }
     }
   }
-  for (size_t i = nrows - rest; i < nrows; ++i) {
-    const size_t rid = row_indices.begin[i];
-    const size_t ibegin = gmat.row_ptr[rid];
-    const size_t iend = gmat.row_ptr[rid + 1];
-    const GradientPair stat = gpair[rid];
-    for (size_t j = ibegin; j < iend; ++j) {
-      const uint32_t bin = gmat.index[j];
-      data_[bin].Add(stat);
+
+  if (nthread_to_process > 1) {
+    const size_t size = (2*nbins_);
+    const size_t block_size = 1024;
+    size_t n_blocks = size/block_size;
+    n_blocks += !!(size - n_blocks*block_size);
+
+    size_t n_worked_bins = 0;
+    for (size_t i = 0; i < nthread_to_process; ++i) {
+      if (thread_init_[i]) {
+        thread_init_[n_worked_bins++] = i;
+      }
     }
-  }
 
-  /* reduction */
-  const uint32_t nbins = nbins_;
-  #pragma omp parallel for num_threads(nthread) schedule(static)
-  for (bst_omp_uint bin_id = 0; bin_id < bst_omp_uint(nbins); ++bin_id) {
-    for (bst_omp_uint tid = 0; tid < nthread; ++tid) {
-      hist.begin[bin_id].Add(data_[tid * nbins_ + bin_id]);
+    #pragma omp parallel for num_threads(std::min(nthread, n_blocks)) schedule(guided)
+    for (bst_omp_uint iblock = 0; iblock < n_blocks; iblock++) {
+      const size_t istart = iblock*block_size;
+      const size_t iend = (((iblock+1)*block_size > size) ? size : istart + block_size);
+
+      const size_t bin = 2*thread_init_[0]*nbins_;
+      memcpy(hist_data + istart, (data + bin + istart), sizeof(double)*(iend - istart));
+
+      for (size_t i_bin_part = 1; i_bin_part < n_worked_bins; ++i_bin_part) {
+        const size_t bin = 2*thread_init_[i_bin_part]*nbins_;
+        for (size_t i = istart; i < iend; i++) {
+          hist_data[i] += data[bin + i];
+        }
+      }
     }
   }
 }
diff --git a/src/common/hist_util.h b/src/common/hist_util.h
index ad83dd6c8e18..30d0454c6454 100644
--- a/src/common/hist_util.h
+++ b/src/common/hist_util.h
@@ -238,6 +238,7 @@ class GHistBuilder {
   inline void Init(size_t nthread, uint32_t nbins) {
     nthread_ = nthread;
     nbins_ = nbins;
+    thread_init_.resize(nthread_);
   }
 
   // construct a histogram via histogram aggregation
@@ -259,6 +260,7 @@ class GHistBuilder {
   /*! \brief number of all bins over all features */
   uint32_t nbins_;
   std::vector<GHistEntry> data_;
+  std::vector<size_t> thread_init_;
 };