The iodine content in milk depends on various factors, including the season, production system, and location of milk production. The aim of this study was 1) to obtain data on the iodine concentration of conventional and organically produced milk and according to seasons; 2) to compare these actual data with previous measurement data; 3) to study the influence of UHT treatment on the iodine content and 4) to estimate the contribution of organic and conventional milk to the consumer’s iodine intake. A total of 110 samples of conventional and organic ultra-heat treated (UHT) whole milk were collected in the period between 1 May 2013 and 30 April 2014 from two large-scale companies, processing milk from two regions in Switzerland. The iodine concentration in organic milk (average 71 ± 25 μg/l) was significantly lower than in conventional milk (average 111 ± 26 μg/l) and varied between suppliers. Milk iodine concentration varied according to the month of collection in organic and conventionally produced milk, with lowest values between August and October (organic milk 42 μg/l; conventional milk 75 μg/l) and highest values in January (organic milk 99 μg/l; conventional milk 145 μg/l). Heat treatment did not influence iodine concentration. Since milk and dairy products are significant source of food-related iodine intake in Switzerland, consumers who prefer organic milk and dairy products are likely to have an inferior iodine status.