Background The objective of the Swedish cleft lip and palate registry (CLP registry) is to promote quality control, research and improvement of treatment, by the comparison of long-term results. The aim was to compare data from the CLP registry among the six treatment centres, regarding data on surgery and speech outcomes at 5 years of age. Methods The participants were 430 children born in Sweden from 2009 to 2014, with cleft palate with or without cleft lip and without known syndromes and/or additional malformations. The number of primary and secondary palatal surgeries up to 5 years of age, timing of the last primary palatal surgery, percentage consonants correct, percentage non-oral speech errors and perceived velopharyngeal competence at 5 years were assessed. Multivariable binary logistic regression adjusted for sex and cleft type was used to compare results between the six centres. Results At one centre (centre 4), the palate was closed in one to three stages, and at the remaining centres in one or two stages. At centre 4, more children underwent a higher number of palatal surgeries, and the last primary palatal surgery was performed at a higher age. Children in centre 4 were also less likely to achieve >= 86% correct consonants (OR = 0.169, P = < 0.001), have no non-oral speech errors (OR = 0.347, P = < 0.001), or have competent or marginally incompetent velopharyngeal competence (OR = 0.244, P = < 0.001), compared to the average results of the other centres. No clear association between patient volume and speech outcome was observed. Conclusions The results indicated the risk of a negative speech result if the last primary palatal surgery was performed after 25 months of age. Whether the cleft in the palate was closed in one or two stages did not affect speech outcome. The Swedish CLP registry can be used for open comparisons of treatment results to provide the basis for improvements of treatment methods. If deviating negative results are seen consistently at one centre, this information should be acted upon by further investigation and analysis, making changes to the treatment protocol as needed.