Iodine is a milk micronutrient whose concentration is highly variable and depends on several factors. The aim of this work was to monitor the prevailing concentration of iodine in raw goat (n = 71) and sheep (n = 68) milk from farms in the Czech Republic, to assess the variation in iodine levels and evaluate them with farming practices, herd size, breed and season. Iodine was determined by a spectrophotometric method according to Sandell-Kolthoff. The mean prevailing iodine concentration in goat and sheep milk was 249.73 and 264.21 μg/L, respectively. In addition to inter-species variability, we found statistically significant differences depending on the both sheep and goat herd size. The differences between conventional and organic farming were relatively minor and without statistical significance.