| Date | Title | Label | |
| 1949-1950 | Snaketimes Rhythm | SMC | Details |
| 1949-1950 | Moondog's Symphony | SMC | Details |
| 1949-1950 | Organ Rounds | SMC | Details |
| 1949-1950 | Obe Rounds | SMC | Details |
| 1953 | Improvisations At A Jazz Concert | Brunswick | Details |
| 1953 | Moondog And His Friends | Epic | Details |
| 1953 | Moondog On The Streets Of New York | Decca/Mars | Details |
| c. 1953 | Surf Session | SMC | Details |
| 1954 | New York 19 | Folkways | Details |
| 1955 | Moondog And His Honking Geese | Moondog Records | Details |
| 1955 | Jazztime USA | Brunswick | Details |
| 1956 | Moondog/Caribea | Prestige | Details |
| 1956 | Caribea | Moondog Records | Details |
| 1956 | More Moondog | Prestige | Details |
| 1957 | The Story Of Moondog | Prestige | Details |
| 1957 | Tell It Again | Angel/Capital | Details |
| 1959 | Moondog Suite | MGM | Details |
| 1969 | Moondog | Columbia | Details |
| 1970 | Fill Your Head With Rock | CBS | Details |
| 1970 | Stamping Ground | CBS | Details |
| 1971 | Moondog 11 | Columbia | Details |
| 1977 | Moondog In Europe | Kopf | Details |
| 1978 | Moondog - Selected Works | Musical Heritage Society | Details |
| 1978 | H'Art Songs | Kopf | Details |
| 1978 | Canons On The Keys | Unreleased | Details |
| 1979 | A New Sound Of An Old Instrument | Kopf | Details |
| 1981 | Facets | MC Managarm | Details |
| 1986 | Bracelli | Kakaphone | Details |
| 1992 | Elpmas | Kopf | Details |
| 1992 | Moondog - Compilation | Columbia | Details |
| 1994 | Sax Pax For A Sax | Kopf | Details |
| 1995 | Big Band | Trimba | Details |
| 1995 | Alphorn Of Plenty | Hat Art | Details |
| 1996 | To A Grain Of Rice | Paradise Records | Details |
| 1997 | Early Music | Nonesuch | Details |
| 1998 | Trees Against The Sky | SHI-RA-Nui 360° | Details |
| 1998 | The Big Lebowski | Mercury | Details |
| 2000 | FSUK Vol. 3 | Unkown | Details |
| 2000 | Moondog Vol. 1 & 2 | Beat Goes On | Details |
| 2000 | Miniatures 2 | Cherry Red | Details |
| 2000 | Noodle Shop Moon Dog Girl | Sparkling Beatnik | Details |
