•HRV is used to assess cardiac autonomic modulation.•HRV is useful to assess the effect of physical exercise programmes.•What are the common shortcomings of using the HRV methodology?•What are the recommendations of using HRV collection and analysis methods?•Checklist regarding the use of the HRV collection and analysis methodology. Heart rate variability is used as an assessment method for cardiac autonomic modulation. Since the Task Force's publication on heart rate variability in 1996, the European Heart Rhythm Association Position Paper in 2015 and a recent publication in 2017, attention has been paid to recommendations on using heart rate variability analysis methods, as well as their applications in different physiological conditions and clinical studies. This analysis has proved to be useful as a complementary tool for clinical evaluation and to assess the effect of non-pharmacological therapeutic interventions, such as physical exercise programmes, on cardiac autonomic modulation. The aim of this article is to make recommendations and to develop a checklist of normalisation procedures regarding the use of heart rate variability data collection and analysis methodology, focusing on the cardiology area and cardiac rehabilitation. Based on previous heart rate variability publications, this paper provides a description of the most common shortcomings of using the analysis methods and considers recommendations and suggestions on how to minimise these occurrences by using a specific checklist. This article includes recommendations and a checklist regarding the use of heart rate variability collection and analysis methods. This work could help improve reporting on clinical evaluation and therapeutic intervention results and consequently, disseminate heart rate variability knowledge.