In response to certain types of DNA damage, ataxia telangiectasia and rad3‐related (ATR) phosphorylates checkpoint kinase 1 (CHEK1) resulting in cell cycle arrest and subsequent DNA repair. ATR and CHEK1 contain mononucleotide microsatellite repeat regions, which are mutational targets in tumors with defective mismatch repair (MMR). This study examined the frequency of such mutations in colon cancers and their impact on biologic behavior. Screening for ATR mutations in 48 tumors was performed using denaturing high‐performance liquid chromatography (DHPLC) and confirmed with sequencing analysis. The CHEK1 exon 7 A(9) region was sequenced in 20 of the 27 (74%) tumors with high frequency of microsatellite instability (MSI‐H). Univariate and multivariate analyses were used to examine associations with clinical outcomes. Frequent mutations in MSI‐H colon cancers were identified within the ATR (37%)/CHEK1(5%) damage response pathway. Stage and MSI status both independently predicted overall survival (OS) and disease‐free survival (DFS). ATR status was not associated with stage, but was associated with a trend toward improved DFS: 0/9 cancers recurred in MSI‐H cases harboring ATR mutations vs. 4/18 recurrences in MSI‐H cases without ATR mutations. This suggests that ATR mutations may affect clinical behavior and response to therapy in MSI‐H colon cancers. © 2007 Wiley‐Liss, Inc.