Our immune system protects us from various pathogens, autoimmune processes and malignancy. Primary immunodeficiency disorders are rare, however in contrast to the conventional perception, primary immunodeficiency diseases are more common than expected and may occur at any age. An insult to the immune system, primary or secondary, may lead to an increased incidence of infectious diseases, autoimmune diseases and malignancies. Primary care physicians, frequently encounter children and adults who suffer from recurrent infections, emphasizing the need for a structured approach for the evaluation of patients with suspected immunodeficiency. The growing knowledge of the fundamental mechanisms and function of the immune system together with recent developments in the field of clinical immunodeficiency enables us to use advanced diagnostic tools for the early diagnosis and treatment of these patients. In this review, we summarize the main aspects and updates of primary and secondary immune deficiency diseases, outline the "red flags" of immunodeficiency states and offer a stepwise workup approach for primary physicians and clinical immunology specialists. Some of the immunodeficiency "red flags" include recurrent infections, invasive infections, atypical pathogens, partial response to antibiotic treatment and frequent use of antibiotics, failure to thrive, chronic diarrhea and fungal infections, unexplained skin rash and a family history.