Although single heterozygous markers in yeast usually segregate during meiosis in a 2:2 ratio, abberant 3:1 segregations occur quite frequently as a result of gene-conversion events. A second type of aberrant segregation, post-meiotic segregation, results from the segregation of two genotypes from a single haploid spore; in yeast such events are detected as sectored spore colonies and usually occur rarely. Post-meiotic segregation is thought to result from the replication of heteroduplex DNA formed during meiotic recombination. We report here that if the heteroduplex includes a palindromic insertion sequence, a high frequency of post-meiotic segregation results. This suggests that palindromic insertions are poorly repaired, which may be the result of hairpin-loop formation that affects the efficiency of repair of heteroduplex DNA.