Although pay differences between men and women with comparable characteristics are generally smaller in the nonprofit than in the for-profit sector, gender pay gaps in the nonprofit sector vary widely across industries. In some industries, gender pay gaps are as large as in the for-profit sector, but in others, women make more than comparably qualified men. Using Hierarchical Linear Modeling on the combined 2001-2006 American Community Surveys, we test nonprofit labor motivation theories against a gendered-job hypothesis to explain this variation. We find that gender pay gaps in the nonprofit sector are smaller in industries where nonprofits outnumber for-profits and where higher proportions of female-dominated occupations exist.