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Background  African animal trypanosomiasis is an economically significant disease that affects the livestock industry in Nigeria. It is caused by several parasites of the genus  Trypanosoma . National estimates of the disease prevalence in livestock and tsetse flies are lacking, therefore a systematic review and meta-analysis were performed to understand the trend of the disease prevalence over the years.    Methods  Publications were screened in Web of Science, Ovid MEDLINE, Global Health, EMBASE and PubMed databases. Using four-stage (identification, screening, eligibility and inclusion) process in the PRIMSA checklist, only studies that met the inclusion criteria for AAT and tsetse infections were analysed. Point estimates prevalence and subgroup analyses based on diagnostic techniques in livestock were evaluated at 95% confidence interval (CI).    Results  A total of 74 eligible studies published between 1960 and 2017 were selected for meta-analysis. This covers the six geopolitical zones, involving a total of 53,924 animals. The overall prevalence of AAT was 16.1% (95% CI: 12.3–20.3%). Based on diagnostic techniques, the prevalence of AAT in cattle was highest in PCR followed by serology and microscopy while the highest prevalence in pigs was observed with serology. Out of 12,552 tsetse flies examined from 14 eligible studies, an overall prevalence of 17.3% (95% CI: 4.5–36.0%) and subgroup prevalence of 49.7% (95% CI: 30.7–68.8%), 11.5% (95% CI: 6.1–18.5) and 4.5% (95% CI: 1.8–8.8%) in  G. morsitans ,  G. tachinoides  and  G. palpalis , respectively, were observed using the random effects-model.    Conclusions  The prevalence of trypanosomes in both vectors and animal hosts was high in Nigeria. Therefore, further research on risk factors, seasonal and transhumance effects, vectoral capacity and competence are warranted for an effective control of AAT in Nigeria.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2801-0) contains supplementary material, which is available to authorized users.

A meta-analysis of the prevalence of African animal trypanosomiasis in Nigeria from 1960 to 2017