We investigated whether kindergarten girls' and boys' (N = 162) motivation for science (perceived competence and liking) differed. Children were ethnically and linguistically diverse, primarily from low‐income families, and attended one of three schools. One school offered a typical kindergarten science experience. Kindergarteners in the other two schools participated in the Scientific Literacy Project (SLP)—a program based on a conceptually coherent sequence of integrated science inquiry and literacy activities. SLP lasted either 5 or 10 weeks. Regardless of sex, both groups of SLP children had greater motivation for science than children who had only the regular science experience. Moreover, children receiving 10 weeks of SLP reported greater science competence than those who received 5 weeks. Boys in regular classrooms reported liking science more than did girls, however there was no sex difference for SLP children. These results are supported by interview data accessing children's ideas about science. The findings suggest that early meaningful participation in science is likely to promote girls' and boys' motivation for science. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 46: 166–191, 2009