Storage of goat milk production in cold temperatures is a current Brazilian legislation request, however there is no specification of a limit period for this. The present work aimed to characterize the microbiological characteristics of raw goat milk produced in a specific region of Brazil, as well as the influence of the storage system and period on its quality. Sixty-one samples from 12 goat farms were collected and subjected to analysis to enumerate hygiene indicator microorganisms, psychrotrophics and proteolytic psychrotrophics. The obtained counts were described and compared considering the system and period of storage (ANOVA, Tukey). Despite presenting low counts of mesophiles, the samples presented high counts of other groups and a relevant presence of proteolytics. Samples collected from bulk tanks presented higher counts of mesophiles and psychrotrophics when compared to immersion tanks and freezers (p < 0.05). When stored for a period of 48 h or longer, the counts of mesophiles, coliforms, Escherichia coli and psychrotrophics were also significantly higher when compared to a storage period of 24 h or less (p < 0.05). The results indicate specific problems in goat milk production in the studied area and the need of establishing a period limit for raw goat milk collection in Brazil.