The main aim of this study was to evaluate the effect of the lactation stage (SL) on the fatty acids (FA) profile of raw milk of Brown Short-haired goats reared under organic regime. An integraf part of the study was also to assess the effect of the SL on the physico-chemical characteristics and somatic cell count (SCC) of milk. Milk records and samplings of each goat were carried out seven times from April to October. SL had a significant effect on contents of almost all monitored physicochemical properties, somatic cell counts (SCC) and FA of milk and also on average daily milk yield (DMY). DMY gradually decreased with advanced lactation (from 3.44 to 1.44 litre), whereas the content of total solids (TS) increased in the course of lactation (from 10.9 to 14.0%). Also the content of milk fat (F) increased in the course of lactation (from 3.2 to 4.7%). Contents of total protein (TP) and casein (C) were relatively high in early lactation, decreased as lactation peaked and increased towards to late lactation (3.7% of TP and 2.6% of C). Titratable acidity (TA) gradually increased from 90th day (6.2°SH) to the end of lactation (8.5°SH), while positive correlations with TS, F, TP,C and lactose were found. SCC increased as lactation advanced, moreover, a positive correlation among SCC and TA and TS was found. The SL had a significant effect on all FA groups. PUFA gradually decreased towards to late lactation, which was caused mainly by the content of linoleic acid. Similarly, the presence of linolenic acid and PUFA/SFA ratio showed a decreasing tendency with advanced lactation. Also the CLA content was the lowest at the end of lactation. PUFA n-6/n-3 ratio increased in mid lactation (7.8) and hereafter decreased towards to late lactation (3.5). In our opinion, a less favourable presence of particular groups of FA in late lactation was related with a decrease in pasture quality under organic conditions.