Aim of the study: To present relevant clinical features of X-linked agammaglobulinaemia (XLA) and common variable immunodeficiency (CVID) in children, helpful in the everyday practice of paediatricians and general practitioners. To analyse the similarities and differences between XLA and CVID. Material and methods: The retrospective analysis of the onset of symptoms, age of clinical diagnosis, basic immunological parameters, and infectious and non-infectious complications in 11 XLA and 21 CVID patients from a single centre was carried out. Results: XLA boys presented the first symptoms in the second half of the first year of life. They had extremely low B-cell numbers (mean: 15 cells/µl, 0.45%), and immunoglobulin levels (median IgG: 0.38 g/l). Patients with CVID presented later occurrence of symptoms (median: two years), higher numbers of B cells (mean: 304 cells/µl, 12.5%), and higher immunoglobulin G levels (median: 2.92 g/l), but lower T CD4 cells. IgM and IgA levels were diminished in both groups, with lower values in XLA patients. Relevant differences (p < 0.05) in B-cell numbers and IgG levels between XLA and CVID groups were observed. Severe clinical complications such as chronic lung disease, bronchiectasis, autoimmune disorders, splenomegaly, and lymphadenopathy were more often observed in CVID. Conclusions: An earlier onset of symptoms, extremely low B-cell numbers and immunoglobulin levels, and normal numbers of T cells point to XLA. Hypogammaglobulinaemia accompanied by non-infectious complications and diminished CD4 T cells are more suggestive of CVID. Greater awareness between paediatricians and general physicians should lead to a proper diagnosis, earlier treatment, avoidance of severe life-threatening complications, and better quality of life.