Evidence suggests affective disorders such as depression and bipolar disorder are characterised by dysregulated autonomic nervous system (ANS) activity. These findings suggest ANS dysregulation may be involved in the pathogenesis of affective disorders. Different affective states are characterised by different ANS activity patterns (i.e., an increase or decrease in sympathetic or parasympathetic activity). To understand how ANS abnormalities are involved in the development of affective disorders, it is important to understand how affective states correlate with ANS activity before their onset. Using heart rate variability (HRV) as a tool to measure ANS activity, this review aimed to look at associations between affective states and HRV in non-clinical populations (i.e., in those without medical and psychiatric disorders). Searches on PubMed and Google Scholar were completed using the following search terms: heart rate variability, autonomic nervous system, sympathetic nervous system, parasympathetic nervous system, affective state, mood and emotion in all possible combinations. All but one of the studies examined (N = 13), demonstrated significant associations between affect and HRV. Findings suggest negative affect, encompassing both diffused longer-term experiences (i.e., mood) as well as more focused short-term experiences (i.e., emotions), may be associated with a reduction in parasympathetic activity as measured through HRV parameters known to quantify parasympathetic activity (e.g., high frequency (HF)-HRV). HRV measures typically linked to reduction in parasympathetic activity appear to be linked to negative affective states in non-clinical populations. However, given the complex and possibly non-linear relationship between HRV and parasympathetic activity, further studies need to clarify specificity of these findings. Future studies should investigate the potential utility of HRV measures as biomarkers for monitoring changes in affective states and for early detection of onset and relapse of depression in patients with affective disorders.