Milk needs to be of good quality and a low somatic cell count (SCC) and absence of contaminants such as aflatoxin M₁ (AFM₁) are important factors in the assessment of the health status of herds. The objective of this study was to evaluate the presence of aflatoxin M₁ and SCC in milk and to determine the correlation between aflatoxin M₁ and SCC. Fifteen lactating cows were monitored at intervals of 15 d over a period of 45 d (n = 4) on 9 dairy farms in the state of São Paulo (n = 540). Milk samples were collected from the glass collecting jars (n = 15) and refrigeration tanks (n = 38). Aflatoxin M₁ was determined on immunoaffinity columns using separation and quantification by high-performance liquid chromatography (HPLC). Somatic cell counting was performed by flow cytometry in a Somacount 300. Data were analyzed using a one-way ANOVA with Tukey’s test (P ≤ 0.05). Pearson correlation test was used between AFM₁ and CCS. Aflatoxin M₁ was detected in 12% (n = 64) of the milk samples collected from the glass bottles. Mean contamination of the samples ranged from 0.03 ± 0.09 to 0.746 ± 1.85 µg/kg, with a maximum level of 9.83 µg/kg. Of the 38 milk samples obtained from the refrigeration tanks, 16% (n = 6) were contaminated with aflatoxin M₁, with levels ranging from 0.44 to 2.65 µg/kg; 83% (n = 4.98) of these samples contained levels that exceeded the limit permitted by the Brazilian legislation (0.5 µg/kg). Mean SCC in the glass collecting bottles ranged from 283.78 (±1,302.12) to 1,124.58 (±1,844.9) x 1,000 cells/mL. Mean SCC in the refrigeration tanks ranged from 452.75 (±220.7) to 2,057.75 (±1,233) x 1,000 cells/mL. All farms had tanks with SCC above the limit permitted by the current Brazilian legislation (500 × 1,000 cells/mL). There was no correlation between the detection of aflatoxin M₁ and SCC in milk samples from the glass collecting jars or refrigeration tanks. The presence of aflatoxin M₁ and high SCC indicate deficiency in the sanitation management of the farms and highlight the need for public policies to improve these patterns.