Lymphoproliferative diseases (LPDs) of the ocular adnexa encompass the majority of orbital diseases and include reactive follicular hyperplasia (RFH), atypical lymphoid hyperplasia (ALH), and mucosa-associated lymphoid tissue lymphoma (MALToma). Lymphoid follicles (LFs) are usually observed during the histological examination of LPDs. Currently, because there is a lack of specific clinical signs and diagnostic immunohistochemical biomarkers, it is difficult for pathologists to distinguish MALToma from ocular RFH and ALH, which makes the clinical management of these conditions difficult. Here, we analyzed the clinical features of patients with ocular adnexal LPDs (n = 125) and investigated the structure of LFs in paraffin-embedded tissue samples using anti-CD23 and anti-IgD immunochemistry. We found that some clinical features including age, sex, and laterality were different among RFH, LFH, and MALToma. Additionally, immunohistochemistry revealed that the expression of IgD and CD23 was higher in RFH patients and decreased in patients with ALH and MALToma. Moreover, LFs in RFH were intact, whereas the structures of most LFs were disrupted in ALH. In MALToma specimens, few intact LFs were observed. In a further investigation, we combined the results for CD23/IgD immunohistochemistry and the structure of LFs to establish a scoring method for the differential diagnosis of LPDs. According to the BIOMED-2 protocol, we further detected IgH gene monoclonal rearrangement in 73 cases (35 RFH, 17 ALH, and 21 MALToma cases). The sensitivity of our scoring method, based on a comparison with the results of IgH gene monoclonal rearrangement detection, was 85.7% (18/21) for MALToma and 35.3% (6/17) for ALH. Our study provides a method that may be useful for the differential diagnosis of RFH, ALH, and MALToma.