Obesity is a major contributor to the dysfunction of liver, cardiac, pulmonary, endocrine and reproductive system, as well as a component of metabolic syndrome. Although development of obesity-related disorders is associated with lipid abnormalities, most previous studies dealing with the problem in question were limited to routinely determined parameters, such as serum concentrations of triacylglycerols, total cholesterol, low-density and high-density lipoprotein cholesterol. Many authors postulated to extend the scope of analysed lipid compounds and to study obesity-related alterations in other, previously non-examined groups of lipids. Comprehensive quantitative, structural and functional analysis of specific lipid groups may result in identification of new obesity-related alterations. The review summarizes available evidence of obesity-related alterations in various groups of lipids and their impact on health status of obese subjects. Further, the role of diet and endogenous lipid synthesis in the development of serum lipid alterations is discussed, along with potential application of various lipid compounds as risk markers for obesity-related comorbidities.