Several studies have reported inconsistent findings for the effect of gender on goiter prevalence. We undertook a systematic review and meta-analysis to investigate the effect of gender on goiter prevalence in different age groups and with differing iodine status. We systematically searched Medline, Embase, the Cochrane Library and Persian databases for trials published between 1950 and May 2012. We included studies assessing the goiter in both genders using palpation or ultrasonography, without age limitation. Summary estimates of pooled prevalence proportions were calculated with a quality effects model. Of 3286 candidate articles, 143 were eligible (606,714 participants). Proportional prevalence of goiter was greater for females than males 0.54 (95 % CI = 0.53-0.56) versus 0.46 (95 % CI = 0.44-0.47), these proportions for subgroups of longstanding iodine deficiency and recent (<10 years) iodine sufficiency were 0.59 versus 0.41 and 0.54 versus 0.46, respectively; however, no gender difference was observed in proportional prevalence of goiter in the subgroup of longstanding (>10 years) iodine sufficiency (0.50 vs. 0.50). These proportions for grade 1 of goiter were 0.54 versus 0.46 and for grade 2 were 0.63 versus 0.37; for children were 0.54 versus 0.46 and for adults were 0.74 versus 0.26 for females and males, respectively. Subgroup analyses showed that there was an increasing trend in gender differences around the age of 15 years. Goiter is more frequent in females. This gender difference in prevalence of goiter is more prominent in iodine-deficient areas, and with grade 2 of goiter, notably after puberty.