Diagnosis of primary lymphomas of the central nervous system (PCNSL) largely depends on histopathology of tumor biopsies. Recently, we identified miRNAs detected in the CSF of PCNSL patients as novel non-invasive biomarkers for this disease. In combined analyses of miR-21, miR-19b, and miR-92 CSF levels, it was possible to differentiate PCNSL from other neurological disorders. In the current study, we first confirmed our previous findings in an enlarged PCNSL cohort (n = 39; sensitivity 97.4 %). Also, we sought to establish the potential role of CSF miRNAs as biomarkers for disease course monitoring. In sequential miRNA measurements in CSF derived from nine patients with different disease courses, an intriguing correlation of miRNA levels and PCNSL status during treatment and/or disease follow-up was demonstrated. Finally, we demonstrated that miRNA levels in serum of PCNSL patients (n = 14) were not elevated as compared to controls. In summary, this study provides the first evidence that CSF miRNAs have the potential as biomarkers for treatment monitoring and disease follow-up of patients with PCNSL.