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Simple Summary: Chronic lymphocytic leukemia (CLL) may be atypical in terms of the cell morphology picture, but also with regard to the surface immunophenotypic profile. Aiming at assessing the impact of morphology and immunophenotype in defining the atypical characteristics of CLL in terms of clinical–biological features and prognosis, a retrospective analysis of a large cohort of CLL patients was performed. We found that morphology better predicts the prognosis of atypical CLL compared to immunophenotypic analysis. Also, discordant cases in terms of immunophenotype and morphology did not identify specific prognostic groups. Overall, the question that still needs to be answered is: does it make sense to focus on morphology and immunophenotypic features in CLL in the era of molecular markers used as prognostic indicators? Atypical chronic lymphocytic leukemia (CLL) is still defined according to morphological criteria. However, deviance from the typical surface immunological profile suggests an atypical immunological-based CLL. A large cohort of patients with CLL was retrospectively evaluated aiming at assessing morphological (FAB criteria), immunophenotypical (two or more discordances from the typical profile), and clinical–biological features of atypical CLL. Compared to typical cases, morphologically atypical CLL showed a greater percentage of unmutated IgVH and CD38 positivity, and a higher expression of CD20. Immunophenotypically atypical CLL was characterized by more advanced clinical stages, higher expression of CD20, higher rate of FMC7, CD79b and CD49d positivity, and by an intermediate–high expression of membrane surface immunoglobulin, compared to typical cases. When patients were categorized based on immunophenotypic and morphologic concordance or discordance, no difference emerged. Finally, morphological features better discriminated patients' prognosis in terms of time-to-first treatment, while concordant atypical cases showed overall a worse prognosis. Discordant cases by immunophenotype and/or morphology did not identify specific prognostic groups. Whether—in the era of molecular markers used as prognostic indicators—it does make sense to focus on morphology and immunophenotype features in CLL is still matter of debate needing further research. [ABSTRACT FROM AUTHOR]