| TM | LM | Artist | Title | Label | |
| 1 | 2 | Sebadoh | The Sebadoh | Sub Pop | |
| 2 | - | Oh Susanna | Johnstown | Stella | c |
| 3 | - | Various | Syrup & Gasoline Vol.1 | Grenadine | c |
| 4 | - | Beth Orton | Central Reservation | BMG | |
| 5 | - | Wilco | Summer Teeth | Warner | |
| 6 | 12 | By Divine Right | Bless This Mess | Nettwerk | c |
| 7 | - | Dinner Is Ruined Band | A Maggot In Their Heads | Sonic Unyon | c |
| 8 | 18 | Legion Of Green Men | Floating In Shallow Water | Post | c |
| 9 | - | Sleater-Kinney | The Hot Rock | Kill Rock Stars | |
| 10 | - | F. Black & The Catholics | Pistolero | Sonic Unyon | |
| 11 | 21 | April March | Chrominance Decoder | Ideal | |
| 12 | 4 | Built To Spill | Keep It Like A Secret | Warner | |
| 13 | - | Low | Secret Name | Kranky | |
| 14 | 7 | Coldcut | Let Us Replay | Ninja Tune | |
| 15 | - | The Mahones | The Hellfire Club Session | True North | c |
| 16 | 39 | John Coltrane | The Classic Quartet | Impulse | |
| 17 | - | The Kingpins | Let's Go To Work | Stomp | c |
| 18 | - | Various | From Dublin To Dakar | PutuAprilo | |
| 19 | - | Blur | 13 | EMI | |
| 20 | - | Propagandhi | Where Quantity Is Job #1 | G-7 Welcoming C. | c |
| 21 | - | Of Montreal | The Gay Parade | Bar None | |
| 22 | 10 | Gob | How Far Shallow Takes You | Fearless | c |
| 23 | 8 | Sparklehorse | Good Morning Spider | Capitol | |
| 24 | - | The Make-Up | I Want Some | K | |
| 25 | 28 | Muslimgauze | Hussein Mahmood Jeeb... | Soleilmoon | |
| 26 | - | Looper | Up A Tree | Sub Pop | |
| 27 | 3 | Ani Difranco | Up Up Up Up Up Up | Righteous Babe | |
| 28 | - | Jazzberry Ram | JR. Adventure | Independent | c |
| 29 | - | Various | Four Dots | Montesano | |
| 30 | - | The Roots | Things Fall Apart | MCA | |
| 31 | - | The Beta Band | The Three EP's | Astral | |
| 32 | - | 122 Greige | Moving Away From The Sun | Teenage USA | c |
| 33 | - | Rudeboy | Shut Up And Dance | Moon | |
| 34 | - | Squarepusher | Budakhan Mindphones | Nothing | |
| 35 | 20 | Autechre | Autechre | Warp | |
| 36 | - | Crash Test Dummies | Give Yourself A Hand | BMG | c |
| 37 | - | Mucho Macho | The Limehouse Link | Beggars Banquet | |
| 38 | - | Paul Westerberg | Suicaine Gratification | EMI | |
| 39 | - | The Living End | The Living End | Reprise | |
| 40 | - | Jim O'Rourke | Eureka | Drag City | |
| 41 | - | Cornelius | FM | Matador | |
| 42 | 13 | John McEntire | Reach The Rock | Hefty | |
| 43 | - | The Molestics | Manufacturing Hokum | King Hokum | c |
| 44 | 36 | Chuck E. Weiss | Extremely Cool | Ryko | |
| 45 | 42 | Various | Stop Racism | Attitude/Asian Man | |
| 46 | 45 | Dallas | Dallas | High Park | |
| 47 | - | Howie Beck | Hollow | 13 Clouds | |
| 48 | - | Dropkick Murphys | The Gang's All Here | Hellcat | |
| 49 | 5 | Big Rude Jake | Big Rude Jake | Attic | |
| 50 | - | Deep Dish | Junk Science | Arista | |
CAPR, CCRS, CFBU, CFRO, CFUV, CHMA, CHSR, CHYZ, CIOI, CITR, CIUT, CJAM, CJMQ, CJSR, CJSW, CKDU, CKMS, CKUL,
Listings reflect airplay for the month of April, 1999, and are weighted according to market size and broadcast range.