This review discusses the development of capillary electrophoresis with laser-induced detection and mass spectrometry techniques for the analysis of urinary oligosaccharides to screen for human oligosaccharidoses and related disorders. Capillary electrophoresis is suitable for the analysis of urinary oligosaccharides. It has a high resolution efficiency, and when it is coupled to a laser-induced fluorescence detector system, it offers an optimal analytical sensitivity. Mass spectrometry techniques have evolved as powerful tools for glycan analyses, are important tools for the analysis of oligosaccharide structures, and offer precise results, analytical versatility, very high sensitivity, high precision and high speed. Mass spectrometry is tolerant of mixtures and is a natural choice for the analysis of this class of molecules. The urine oligosaccharide profiles from healthy controls and patients diagnosed with different lysosomal storage diseases (fucosidosis, α-mannosidosis, GM1 gangliosidosis, GM2 gangliosidosis type Sandhoff, glycogen storage disease type 2 and 3, aspartylglucosaminuria, Schindler disease and galactosialydosis) and related disorders (glycogen storage diseases) are presented. In summary, these procedures are powerful tools for the rapid identification and characterization of these disorders. In all cases, the oligosaccharide profiles are strongly informative, identified the abnormal compounds, and are good alternatives to traditional screening tests that use thin layer chromatography. These tests have great sensibility and resolution and are automatable, enabling extended screening of these diseases, both as a first step in diagnosis or for confirming the pathogenicity of mutations that may be detected with next generation sequencing techniques.