We investigated six new cases of primary thymic extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT) to further characterize the clinicopathological and genetic features. The male to female ratio was 1:1. One female patient had suffered from systemic lupus erythematosus. Another female patient was diagnosed with rheumatoid arthritis after thymectomy. One patient had a concurrent tumor in the eyelid. Radiologically, all tumors were located in the prevascular space and presented as asymmetric heterogeneously enhanced cystic and solid masses. MALT1, BCL10 or IGH translocations and trisomy 18 were not observed in any cases by fluorescence in situ hybridization (FISH) analysis. Trisomy 3 was detected in one patient and another showed a TNFAIP3/A20 deletion. Meta-analysis (n = 51) including the present and previously reported cases revealed that the prevalence of autoimmunity was much lower in males with thymic MALT lymphoma compared to females (33% vs. 87%, p = 0.001). Additionally, the average age of females or patients with autoimmunity was about 10 years younger than that of males or patients without autoimmunity (p = 0.003 and p = 0.008, respectively). In summary, thymic MALT lymphoma arising without underlying autoimmunity frequently involves males or older patients. Trisomy 3 and an A20 deletion might play a role in the pathogenesis of thymic MALT lymphoma.