| Diagnosis | Omim Number | Sample Count |
| LACTIC ACIDOSIS, CONGENITAL INFANTILE | 245400 | 3 |
| LANGER MESOMELIC DYSPLASIA | 249700 | 7 |
| LEBER CONGENITAL AMAUROSIS 1; LCA1 | 204000 | 4 |
| LEBER OPTIC ATROPHY | 535000 | 3 |
| LEIGH SYNDROME; LS | 256000 | 42 |
| LEOPARD SYNDROME | 151100 | 4 |
| LEPRECHAUNISM | 246200 | 11 |
| LESCH-NYHAN SYNDROME; LNS | 300322 | 50 |
| LETTERER-SIWE DISEASE | 246400 | 1 |
| LEUKEMIA, CHRONIC MYELOID; CML | 608232 | 1 |
| LEUKEMIA, SUB-ACUTE | | 1 |
| LEUKODYSTROPHY, HYPOMYELINATING, 22; HLD22 | | 1 |
| LEUKOENCEPHALOPATHY WITH VANISHING WHITE MATTER; VWM (OVARIOLEUKODYSTROPHY, INCLUDED) | 603896 | 3 |
| LIG4 SYNDROME | 606593 | 3 |
| LIPASE DEFICIENCY, COMBINED | 246650 | 2 |
| LIPASE, CONGENITAL ABSENCE OF PANCREATIC | 246600 | 4 |
| LIPOID PROTEINOSIS OF URBACH AND WIETHE | 247100 | 1 |
| LONG QT SYNDROME 3; LQT3 | | 1 |
| LONG-CHAIN 3-HYDROXYACYL-CoA DEHYDROGENASE DEFICIENCY | 609016 | 1 |
| LOW-GGT PROGRESSIVE FAMILIAL INTRAHEPATIC CHOLESTASIS (NOT FURTHER CHARACTERIZED) | | 5 |
| LOWE OCULOCEREBRORENAL SYNDROME; OCRL | 309000 | 2 |
| LYMPHOBLASTIC LEUKEMIA, ACUTE, WITH LYMPHOMATOUS FEATURES; LALL | 247640 | 2 |