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Trypanosomosis remains a major challenge to livestock production in much of tropical Sub-Saharan Africa, while diagnosis and treatment still depend on inefficient parasitological techniques. Endemic infections depend on animal reservoirs with subclinical parasitemia. We report molecular diagnosis of subclinical Trypanosoma vivax (T. vivax) infection using polymerase chain reaction (PCR) for the first time in Nigerian goats and associate parasite presence with gross physiological traits and serum metabolites in extensively managed Nigerian goats. PCR was used to amplify a 400 bp DNA fragment of the parasite genome in 205 goats across three geographical zones of the country. Results showed a high subclinical infection rate (SCIR) of 71.7% in the total goats examined. Overall SCIRs of 71%, 75.9% and 55.6% were recorded in West African Dwarf, Red Sokoto and Sahel goats respectively, while geographical SCIRs were 71.2% (Southwest), 75% (Northwest) and 70% (Northeast). T. vivax presence had significant (P < 0.05) effect on respiratory rate and is associated with higher creatinine levels in sera. Logistic regression analyses with Hosmer-Lemeshow goodness-of-fit showed that respiratory rate is the most important predictive trait for the presence of T. vivax infection (P < 0.05). Goats appear to be a viable reservoir for T. vivax infection of other livestock. Molecular diagnosis of subclinical trypanosomosis using PCR could be useful for large scale epidemiological studies, early diagnosis of subclinical infection and treatment of the disease in extensively managed tropical goats.