Background. Estimation of survival requires follow-up of patients from diagnosis until death ensuring complete and good quality data. Many population-based cancer registries in low- and middle-income countries have difficulties linking registry data with regional or national vital statistics, increasing the chances of cases lost to follow-up. The impact of lost to follow-up cases on survival estimates from small population-based cancer registries (<500 cases) has been understudied, and bias could be larger than in larger registries. Methods. We simulated scenarios based on idealized real data from three population-based cancer registries to assess the impact of loss to follow-up on 1-5-year overall and net survival for stomach, colon, and thyroid cancers—cancer types with very different prognosis. Multiple scenarios with varying of lost to follow-up proportions (1-20%) and sample sizes of (100-500 cases) were carried out. We investigated the impact of excluding versus censoring lost to follow-up cases; punctual and bootstrap confidence intervals for the average bias are presented. Results. Censoring of lost to follow-up cases lead to overestimation of the overall survival, this effect was strongest for cancers with a poor prognosis and increased with follow-up time and higher proportion of lost to follow-up cases; these effects were slightly larger for net survival than overall survival. Excluding cases lost to follow-up did not generate a bias on survival estimates on average, but in individual cases, there were under- and overestimating survival. For gastric, colon, and thyroid cancer, relative bias on 5-year cancer survival with 1% of lost to follow-up varied between 6% and 125%, 2% and 40%, and 0.1% and 1.0%, respectively. Conclusion. Estimation of cancer survival from small population-based registries must be interpreted with caution: even small proportions of censoring, or excluding lost to follow-up cases can inflate survival, making it hard to interpret comparison across regions or countries.