Despite the high economical importance of goat milk production in certain regions, the real burden of subclinical mastitis caused by intramammary infections (IMI) is still unknown. This is mainly caused by the lack of reliable diagnostic tests, since the accuracy of somatic cell count (SCC) as an indirect indicator of udder health is questionable in this species. This study aimed to investigate the correlation among and somatic cell count (SCC), total bacterial count (TBC), California Mastitis test (CMT) and microbiological culture (MC) as indicators of udder health in dairy goats in Northeastern Brazil, the leading goat milk producing region in South America. From 6 farms, a total of 396 milk samples were individually collected from each teat of 66 goats at different lactation periods (begining, mid, end). Out of 146 (37%) positive samples, coagulase negative (CoNS, 73%) and positive Staphylococcus (21%), gram-positive bacilli (6%), streptococci (3.4%) and Enterobacteriaceae (1.4%) were identified. SCC and TBC were correlated (r = 0.47; P < 0.01) but a weak correlation (0.20; P < 0.01) was observed between SCC and infection by CoNS infection. Although a positive association (P < 0.05) was seen between SCC and MC using percentile 75 (6.05 log SCC/mL) as threshold, SCC was weakly (0.29) correlated with MC. Interestingly, the correlation was strong at the beginning of lactation (0.49, P < 0.001) but negligible at mid (0.3; P = 0.79) and end lactation (0.12; P = 0.14). Using MC as the gold standard, sensitivity values for CMT and SCC were 39.2 and 40.2%, whereas specificity reached 80 and 89.5%. SCC in non-infected goats increased (P < 0.01) at the end lactation. The low agreement among the diagnostic methods and the large physiological variations in SCC during lactation reinforce the limitations of the current methods to accurately predict udder health in goats, especially at the animal level. A better knowledge about the glandular tissue responses against IM agents is strongly needed. We have currently been using metagenomic approaches to investigate in-depth changes in the microbiome of naturally infected animals to bring new insights about mastitis in goats.