The aim of the study was to evaluate the influence of the milking phase on somatic cell count (SCC) in milk obtained from the cisternal and alveolar parts of udders of selected Polish Holstein-Friesian cows. The study also assessed the impact of other genetic and environmental factors on SCC variability in cisternal and alveolar milk, including: the individual cow, lactation stage, age of cow, production level, milking speed, fat-to-protein ratio, and milking type. The research included 15 cows of Polish Holstein-Friesian breed at different ages, lactation stages, and with varying daily milk yield. A total of 210 milk observations were conducted, including 105 for 1 min milking and 105 for 8 min milking. The results obtained in the study indicated that milk obtained during two different milking phases exhibited similar SCC levels (F for LOGSCC = 0.79). The average actual SCC in milk produced by 15 cows in 105 observations for 1 min milking was 219,000 cells/mL, while for 8 min milking it was 229,000 cells/mL. The results were inconclusive, suggesting that SCC in cisternal and alveolar milk must be influenced by factors other than the milking phase. The analysis of variance conducted for this purpose provided the basis for stating a highly statistically significant effect of the individual cow (F for LOGSCC = 147.9), lactation stage (F for LOGSCC = 54.64), age of cow (F for LOGSCC = 12.39), daily production level (F for LOGSCC = 34.49), milking speed (F for LOGSCC = 17.56), and fat-to-protein ratio (F for LOGSCC = 22.99) on the variability of characteristics defining SCC in milk. In summary, SCC is characterized by high variability, influenced by a range of environmental and genetic factors such as the individual cow, lactation stage, age of cow, milking speed, and dietary fat-to-protein ratio. The influence of milking phase (1 min or 8 min) and milking type (morning or evening) should be considered inconclusive based on the entire population studied. For half of the cows, SCC in cisternal milk was higher than in alveolar milk, while for the other half, the situation was reversed. Further observations are required to confirm the hypothesis regarding the extent to which cows' immunological response to bacterial infections is concentrated in the cisternal or alveolar part of the udder under national environmental conditions.