The pelvic skeleton of threespine stickleback fish contributes to defence against predatory vertebrates, but rare populations exhibit vestigial pelvic phenotypes. Low ionic strength water and absence of predatory fishes are associated with reduction of the pelvic skeleton, and lack of Pitx1 expression in the pelvic region is evidently the genetic basis for pelvic reduction in several populations. Pelvic vestiges in most populations are larger on the left (left-biased), apparently because Pitx2 is expressed only on that side. We used whole-mount in situ hybridization to study Pitx1 expression in 19 populations of Gasterosteus aculeatus from lakes around Cook Inlet, Alaska, USA. As expected, specimens from six populations with full pelvic structures usually expressed Pitx1 in the limb bud; those from eight populations with left-biased pelvic reduction usually did not express it. Specimens from one of three populations with right-biased or unbiased pelvic reduction sometimes expressed Pitx1. One of two populations in which the pelvic spines (but not the girdle) are usually absent often expressed Pitx1. In terms of Jacob's 1977 'tinkering' metaphor, Pitx1 was the spare part with which natural selection usually tinkered for stickleback pelvic reduction, but it also tinkered with other genes that have smaller effects.