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Introduction Bovine tuberculosis (BTB) is widespread yet poorly controlled in Nigeria hence posing a public health threat. This study determined the prevalence of Mycobacterium tuberculosis complex (MTC) and factors associated with MTC among slaughtered cattle at Jos South Abattoir in Plateau State, Nigeria. Methods We conducted a cross sectional study in which we collected 168 lung samples systematically from 485 slaughtered cattle from May-June, 2012, and tested for acid fact bacilli (AFB) using Ziehl-Neelsen test and a duplex polymerase chain reaction technique (PCR) for MTC detection. Data on cattle socio-demographic characteristics and risk factors for zoonotic BTB infection was obtained and analyzed using Epi info version 3.5.3 to determine frequency, proportions, and prevalence odds ratios. Multiple logistic regression was done at 95% Confidence Interval (CI). Results The mean age of the cattle was 5.6 ± 1.3 years and (108) 64.3% were females. Majority were indigenous White Fulani breed of cattle (58.5%) and about half (54.8%) were slightly emaciated. Prevalence of MTB complex was 21.4% by AFB test and 16.7% by duplex PCR. Of 33 (19.6%) lungs with lesions, 27 (81.8%) were positive for AFB; while of 135 (80.4%) lungs without lesions, 9 (6.7%) were positive for AFB. Lungs with lesions were 52 times more likely to test positive to AFB test compared to tissues without lesions (AOR=52.3; 95% CI: 16.4-191.8) Conclusion The presence of MTC in cattle signifies its potential risk to public health. Presence of lesions on lungs is a reliable indicator of MTC infection that meat inspectors should look out for.