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Introduction Published guidance recommends that all girls with inguinal hernia should be screened for complete androgen insensitivity syndrome (CAIS). We report a novel, noninvasive screening technique. Methods Retrospective review of all girls undergoing inguinal herniotomy from April 2009 to October 2010. Those screened using the novel technique of extraction of Y chromosome specific DNA from a buccal mucosal sample obtained by mouth brushing are reported. Results A total of 29 girls were screened by mouth brushing at median age 2.9 years (range 29 days to 9.3 years). Of the 29 samples, 25 were adequate for DNA extraction; 4 were inadequate and screening was repeated (3 repeat mouth brushing, 1 perioperative blood test). Mouth brushing was well tolerated by children and acceptable to parents. A preoperative blood test was avoided in all girls who had a mouth brushing. None of the girls in this study had CAIS. Turn-around time for mouth brushing was mean 4.9 days compared with a minimum of 10 days for a karyotype. This technique is cheaper than a karyotype (£87 vs. £205). Conclusion Extraction of Y chromosome specific DNA from a mouth brushing sample is effective for screening girls with inguinal hernia for CAIS. It is acceptable, cheaper, and quicker than alternatives. [ABSTRACT FROM AUTHOR]