Index: lib/Analysis/ScopDetection.cpp
===================================================================
--- lib/Analysis/ScopDetection.cpp
+++ lib/Analysis/ScopDetection.cpp
@@ -532,7 +532,7 @@
   if (IntToPtrInst *Inst = dyn_cast<IntToPtrInst>(BaseValue))
     return invalid<ReportIntToPtr>(Context, /*Assert=*/true, Inst);
 
-  if (PollyUseRuntimeAliasChecks || IgnoreAliasing)
+  if (IgnoreAliasing)
     return true;
 
   // Check if the base pointer of the memory access does alias with
@@ -548,8 +548,27 @@
   // alias, if -basicaa is not available. They actually do not, but as we can
   // not proof this without -basicaa we would fail. We disable this check to
   // not cause irrelevant verification failures.
-  if (!AS.isMustAlias())
+  if (!AS.isMustAlias()) {
+    if (PollyUseRuntimeAliasChecks) {
+      bool CanBuildRunTimeCheck = true;
+      // The run-time alias check places code that involves the base pointer at
+      // the beginning of the SCoP. This breaks if the base pointer is defined
+      // inside the scop. Hence, we can only use it if we are sure the base
+      // pointer is not an instruction defined inside the scop.
+      for (const auto &Ptr : AS) {
+        Instruction *Inst = dyn_cast<Instruction>(Ptr.getValue());
+        BaseValue->dump();
+        if (Inst && Context.CurRegion.contains(Inst)) {
+          CanBuildRunTimeCheck = false;
+          break;
+        }
+      }
+
+      if (CanBuildRunTimeCheck)
+        return true;
+    }
     return invalid<ReportAlias>(Context, /*Assert=*/false, &Inst, AS);
+  }
 
   return true;
 }
Index: test/ScopDetect/run_time_alias_check.ll
===================================================================
--- /dev/null
+++ test/ScopDetect/run_time_alias_check.ll
@@ -0,0 +1,36 @@
+; RUN: opt %loadPolly -polly-detect -polly-code-generator=isl -analyze < %s | FileCheck %s
+
+target datalayout = "e-p:64:64:64-i1:8:8-i8:8:8-i16:16:16-i32:32:32-i64:64:64-f32:32:32-f64:64:64-v64:64:64-v128:128:128-a0:0:64-s0:64:64-f80:128:128"
+target triple = "x86_64-unknown-linux-gnu"
+
+declare float* @getNextBasePtr(float*) readnone nounwind
+
+define void @base_pointer_is_inst_inside_invariant_1(i64 %n, float* %A, float* %B) {
+entry:
+  br label %for.i
+
+for.i:
+  %indvar.i = phi i64 [ %indvar.i.next, %for.i.inc ], [ 0, %entry ]
+  br label %S1
+
+S1:
+; To get an instruction inside a region, we use a function without side
+; effects on which SCEV blocks, but for which it is still clear that the
+; return value remains invariant throughout the whole loop.
+  %ptr = call float* @getNextBasePtr(float* %A)
+  %conv = sitofp i64 %indvar.i to float
+  %arrayidx5 = getelementptr float* %ptr, i64 %indvar.i
+  store float %conv, float* %arrayidx5, align 4
+  store float 1.0, float* %B
+  br label %for.i.inc
+
+for.i.inc:
+  %indvar.i.next = add i64 %indvar.i, 1
+  %exitcond.i = icmp ne i64 %indvar.i.next, %n
+  br i1 %exitcond.i, label %for.i, label %exit
+
+exit:
+  ret void
+}
+
+; CHECK-NOT: Valid Region for Scop