The evaluation of left ventricular (dys)function is at the core of clinical cardiology practice in patients with hypertrophic cardiomyopathy. Hypertrophic cardiomyopathy proceeds along paradigms that are profoundly different and follows disease-specific patterns of progression towards heart failure. By automatically applying a standard approach, much information is lost or misplaced, and severe degrees of dysfunction may be erroneously interpreted as mild by such an assumption. This is mostly evident during the assessment of systolic function, in which a superficial evaluation of standard variables, often relatively preserved (even in advanced stages), may lead to underestimation of clinical severity, with potential consequences, such as late referral for transplantation. Currently, specific biomarkers–particularly N-terminal prohormone of B-type natriuretic peptide and high-sensitivity cardiac troponin I–play a key role in the diagnosis, treatment and risk stratification of hypertrophic cardiomyopathy. Elevated biomarkers seem to depict patients with more severe disease, adding diagnostic and prognostic information to conventional assessments, such as left ventricular ejection fraction, New York Heart Association class and left ventricular outflow tract obstruction. For all these reasons, we provide a review of current knowledge on systo-diastolic function in patients with hypertrophic cardiomyopathy, in an attempt to define clinically significant degrees of dysfunction, biomarker status and specific “red alert” thresholds in clinical practice.