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Obesity is a major issue affecting not only adults but also children in many places of the world. There are numerous methods for estimating the body fat percentage, however, all of those methods are different in terms of availability, accuracy, and the cost of an individual examination. The aim of this study was to compare two relatively easy and widespread measurement methods for assessing skinfold thickness: the BodyMetrix BX2000 ultrasound machine and a classic GPM caliper. Fifty-eight young women aged 19–24 years with normative body weight participated in the study. We found that although the measurements performed by both methods are positively correlated, the obtained values were different. In seven out of nine measured points, these differences were statistically significant. The measurements of skin fat folds with a caliper showed a higher value of subcutaneous tissue compared to ultrasound measurements. Only the values of measurements on the pectoral and mid-axillary did not differ between the methods. We conclude that due to the significant discrepancies in the values of measured skinfold thickness, appropriate measurement tools and dedicated formulas estimating the amount of body fat should be used.