The activation-induced cytidine deaminase (AID) initiates Ig gene hypermutation by converting cytosine to uracil (U) and generating a U:G lesion. Genetic and biochemical studies suggest that the AID-triggered U:G lesions are processed by three mutagenic pathways to induce mutations at both C:G and A:T pairs. First, direct replication of the U:G lesion leads to C to T and G to A transitions. Second, U can be excised by the uracil DNA glycosylase (UNG) and the replication/processing of the resulting abasic site leads to transversions and transitions at C:G pairs. Third, the U:G lesion is recognized by an atypical mismatch repair (MMR) pathway which generates mutations at A:T pairs in a DNA polymerase η (POLH)-dependent manner. To further explore whether these three mutagenic pathways function competitively or independently, we have analyzed Ig gene hypermutation in mice deficient in both UNG and POLH. Compared with WT mice, UNG deficiency caused elevated frequency of C:G mutations, suggesting that UNG-mediated U excision led to error-free as well as error-prone repair. In contrast, UNG deficiency did not affect the frequency and patterns of A:T mutations, suggesting that the MMR did not target U:G lesions normally recognized and processed by UNG. In addition, POLH deficiency did not affect the frequency and patterns of C:G mutations and UNG POLH double deficiency showed an additive effect of single deficiency. Based on these observations and previous results, along with the recent finding that UNG excises AID-triggered U predominantly during G1 phase of the cell cycle, it appears that UNG and MMR targets U:G lesions generated during G1 and S phases of the cell cycle, respectively.