BACKGROUND: Shigella remains one of the most common causes of diarrhoea in South Asia. Current estimates of the prevalence of Shigella are critical for guiding control measures. We estimated the prevalence of Shigella species and serogroups in South Asia. METHODS: We performed a systematic review using PubMed, EMBASE, Google Scholar, and Web of Science for peer-reviewed studies published between 2000 and June 19, 2022. We also manually searched the reference lists of the reviewed studies to identify additional studies. We included studies that detected the presence of Shigella in stool by culture or polymerase chain reaction (PCR). Studies associated with outbreaks were excluded. Two investigators independently reviewed the studies, extracted the data, and performed quality assessment. A random-effects meta-analysis was performed to determine the pooled prevalence of Shigella. RESULTS: Our search yielded 5707 studies, of which 91 studies from five South Asian countries were included in the systematic review, 79 in the meta-analysis of Shigella prevalence and 63 in the meta-analysis of Shigella serogroups prevalence. The pooled prevalence of Shigella was 7% (95% CI: 6-7%), with heterogeneity (I2 = 98.7; p < 0.01). The prevalence of Shigella was higher in children aged < 5 years (10%; 95% CI: 8-11%), in rural areas (12%; 95% CI: 10-14%), and in studies using PCR (15%; 95% CI: 11-19%). Shigella flexneri (58%) was the most abundant serogroup, followed by Shigella sonnei (19%), Shigella boydii (10%), and Shigella dysenteriae (9%). S. flexneri 2a was the most frequently isolated serotype (36%), followed by serotype 3a (12%), serotype 6 (12%), and serotype 1b (6%). The prevalence of non-typeable Shigella was 10.0%. CONCLUSIONS: Although the prevalence of Shigella in South Asia remains generally high, it varies by age group and geographical area, with data lacking in some countries. Effective Shigella vaccines would be advantageous for both endemic communities and travellers.