New affinity monolithic capillary columns with 150 um internal diameter were prepared in situ fused glass capillary via either immobilization or encapsulation of Candida antarctica lipase B (CALB) on or within polymer monoliths, respectively. The prepared capillary columns (ID 150 um) were investigated for the enantioselective nano liquid chromatographic separation of a set of different classes of racemic pharmaceuticals namely α- and β-blockers, antiinflammatory drugs, antifungal drugs, dopamine antagonists, norepinephrine-dopamine reuptake inhibitors, catecholamines,  sedative hypnotics, diuretics, antihistaminics, anticancer drugs and antiarrhythmic drugs. Run-to-run repeatability was quite satisfactory. The encapsulated lipase-based capillary monolith showed better enantioselective separations of most of the investigated compounds. Baseline separation was achieved for alprenolol, atenolol, bromoglutithimide, carbuterol, chloropheneramine, cizolertine carbinol, 4-hydroxy-3-methoxymandelic acid, desmethylcizolertine, nomifensine, normetanephrine and sulconazole under reversed phase chromatographic conditions. A speculation about the understanding of the chiral recognition mechanism of lipase-based monoliths toward the investigated pharmaceuticals is suggested.