Zebrafish are currently the second most used model for biomedical research and their use shows no sign of abating. Despite this rapid rise in use, relatively little is known about their true welfare requirements and guidelines pertaining to their husbandry needs are broad, leading to husbandry practices becoming varied and non-standardised. In 2012, we developed a health monitoring system based upon body scoring for zebrafish in an attempt to create a more standardised health-monitoring program at UCL. More recently we referenced our health monitoring program against a PCR and histological screen and looked at areas of compatibility, where phenotypical signs of illness and disease, as determined by the health monitoring program, correlated to disease determined by the results of PCR and histological testing. In most cases, fish expressing a disease phenotype were shown to have the corresponding disease by PCR and / or histological analysis; in a small number of cases this proved not to be true - fish expressing phenotypes associated with specific diseases were healthy by PCR and histological analysis and showed no sign of disease. Preliminary database analysis of the fish showing disease phenotypes, but which were not detected by PCR or histology, suggested that specific phenotypes could be associated with specific strains of fish and age of individual fish.  We believe that we have a method of assessing subtle severity limits in fish and distinguishing this from phenotypes that are caused by disease. By using a combination of the body scoring health monitoring program, PCR and histological screening and analysis of patterns of zebrafish ill health found within our database, we are able to refine phenotypic severity limits by creating new endpoints before these phenotypes are expressed.