Introduction/Objective Isolated hypertransaminasemia (IHTS) is a common, benign, and transient appearance in patients with celiac disease (CD). The aim of this study is to determine the frequency of IHTS in children up to two years old with clinically classical CD, as well as its connection with the onset of the first symptoms of the disease, the age of diagnosis, the clinical and laboratory nutritional parameters, and the degree of damage of small intestinal mucosa. Methods The study was based on a sample of 82 children, 55 female and 27 male, ages 7-24 (14.28 ± 4.41) months. The diagnosis of CD was based on the revised ESPGHAN criteria and the activity of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) by standard laboratory methods. Results IHTS was found in 39 (47.56%) patients, 27 of whom (69.23%) had elevated levels of both transaminases and 12 of only one-eight of AST and four of ALT. The increase in relation to the aforementioned reference value for ALT was 1.1-10.08 (1.67 ± 1.73), and for AST it was 1.08-7.91 (1.56 ± 1.29) times. In patients with IHTS compared to those with normal transaminasemia, the age of onset of CD was significantly lower (9.83 ± 3.69 vs. 12.95 ± 4.43 months, p = 0.001), as well as the age of diagnosis (12.97 ± 3.88 vs. 15.47 ± 4.56 months; p = 0.01), while the differences in the other observed parameters were not significant. Conclusions IHTS occurs in almost half of children up to two years old with classical CD. Hypertransaminasemia is in most cases mild and significantly more frequent in patients with earlier clinical expression of the CD.