Chiari-like malformation (CM), syringomyelia (SM) and middle ear effusion (also called PSOM) are three conditions that frequently occur in Cavalier King Charles Spaniels (CKCS). Both CM and SM are currently screened in the Netherlands prior to breeding and are graded according to the British Veterinary Association’s Kennel Club (BVA/KC) scheme. This study evaluated the prevalence and estimated genetic parameter of CM, SM and middle ear effusion from 12 years of screening results. For SM, the classical method using the BVA/KC scheme, was compared with exact measuring of the central canal dilation. For CM, the BVA/KC scheme was compared with a more detailed scheme. Next to this the presence of microchip artifacts was assessed. 1249 screening of 1020 dogs were re-evaluated. Results indicated the presence of CM in all dogs, suggesting it has become a breed-specific characteristic. And although different grades of CM were observed, the condition did not deteriorate over time. SM was present in 39% of the dogs and a clear age effect was demonstrated, with SM increasing with age. This emphasizes the importance of screening at appropriate age, since SM can worsen with increasing age. One alternative is to promote repeated measures. The presence of middle ear effusion in this study was 19%–21% for dogs younger than 3 years, and 32%–38% for dogs older than 3 years. In as much as 60%, microchip artifacts were noticed, leading to the recommendation to place microchips in another location in breeds that are susceptible to developing SM. Finally, this study estimated the heritability of CM in this population, due to the lack of phenotypic variance, to be very low at 0.02–0.03. The heritability for SM central canal dilatation to be 0.30, compared to 0.13 for the classical BVA/KC method, using a model including the age effect and the combined effect of veterinary clinic and year of the evaluation. Genetic correlations were rather small, ranging from 0.16–0.33. As a conclusion, screening for SM and CM in the entire population should be maintained, and a selection scheme against SM should be based on estimated breeding values for the exact measurement of the central canal dilatation.